Overview

Questions

  • What is UPPMAX?

  • What is SNIC/NAISS?

  • What is a cluster?

Objectives

  • We’ll get an overview of UPPMAX and SNIC/NAISS and how a computer cluster works

Instructor note

  • Approx timing: 9:15-9:30

  • Theory

UPPMAX = UppMACS

NAISS

  • National Academic Infrastructure for Supercomputing in Sweden

  • Mission: to provide a quality high-performance computing environment nationally

  • Starting 1 January 2023, the National Academic Infrastructure for Supercomputing in Sweden (NAISS) is the new organization for high-performance computing, storage, and date services for academic users in Sweden.

    • Replaces SNIC — the Swedish National Infrastructure for Computing

    • Linköping university is the host organization for NAISS, but NAISS acts independently with a national perspective and responsibility.

  • From the users perspective, there will initially only be minimal differences between the SNIC and NAISS regimes.

  • Application rounds: https://supr.naiss.se/round/

  • NAISS and Uppsala University fund UPPMAX — UU’s supercomputing center.

UPPMAX missions

  • Runs the clusters placed in Uppsala.

  • More details in the afternoon about Organisational orienteering!

UPPMAX systems

  • Clusters

    • Rackham (general purpose)

      • Snowy (Long runs and GPU:s)

    • Bianca (sensitive data)

      • Miarka (NGI production)

        • genomic data from the sequencing machines are pre-processed before they are delivered to the researcher.

  • Storage

    • On-load, directly connected to the clusters

    • Off-load, for large data not needed for computation analysis anymore

  • Cloud

    • Dis (region EAST-1)

High Performance Computing — HPC

What is a cluster?

  • A network of computers, each computer working as a node.

  • From small scale RaspberryPi cluster…

RaspBerry

  • To supercomputers like Rackham.

Rackham

  • Each node contains several processor cores and RAM and a local disk called scratch.

Node

  • The user logs in to login nodes via Internet through ssh or ThinLinc.

    • Here the file management and lighter data analysis can be performed.

RaspBerry

RaspBerry

  • The calculation nodes have to be used for intense computing.

Overview of the UPPMAX systems

graph TB Node1 -- interactive --> SubGraph2Flow Node1 -- sbatch --> SubGraph2Flow subgraph "Snowy" SubGraph2Flow(calculation nodes) end thinlinc -- usr-sensXXX + 2FA + VPN ----> SubGraph1Flow terminal -- usr --> Node1 terminal -- usr-sensXXX + 2FA + VPN ----> SubGraph1Flow Node1 -- usr-sensXXX + 2FA + no VPN ----> SubGraph1Flow subgraph "Bianca" SubGraph1Flow(Bianca login) -- usr+passwd --> private(private cluster) private -- interactive --> calcB(calculation nodes) private -- sbatch --> calcB end subgraph "Rackham" Node1[Login] -- interactive --> Node2[calculation nodes] Node1 -- sbatch --> Node2 end

Keypoints

  • NAISS makes available large-scale high-performance computing resources, storage capacity, and advanced user support, for Swedish research.

  • UPPMAX runs the local resources placed at Uppsala Universtiy

  • A cluster consists of several inter-connected computers that can work individually or together.